informativeSites: informativeSites

In chutter/FilterZone: R Package For Detecting the Anomaly Zone and Alignment Filtering in Large Phylogenomic Datasets

Description

Calculates the number or proportion of parsimony informative sites in an alignment

Usage

informativeSites(alignment = NULL, count = TRUE, ambiguities = TRUE)

Arguments

alignment	alignment in ape DNABin or a matrix format
count	Whethe to return the count of parsimoney informative sites (TRUE) or the proportion (FALSE)
ambiguities	Whether to consider ambiguities (TRUE) or not (FALSE)

Value

plots the phylogenetic tree and selected data associated with an AstralPlane object. Can optionally be saved to file as a PDF by giving save.file a file name.

Examples

your.tree = ape::read.tree(file = "file-path-to-tree.tre")
astral.data = astralPlane(astral.tree = your.tree,
                          outgroups = c("species_one", "species_two"),
                          tip.length = 1)

chutter/FilterZone documentation built on Dec. 19, 2021, 4:07 p.m.